Abstract

Background

The centromeric and pericentromeric regions of plant chromosomes are colonized by
Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences,
form the chromovirus CRM clade. Despite their potential importance for centromere
evolution and function, they have remained poorly characterized. In this work, we
aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on
their diversity, structure, chromosomal distribution and transcriptional activity.

Results

We have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon
families, derived from 33 host species and falling into 12 plant families. The sequences
at the C-terminus of their integrases were unexpectedly heterogeneous, despite the
understanding that they are responsible for targeting to the centromere. This variation
allowed the division of the CRM clade into the three groups A, B and C, and the members
of each differed considerably with respect to their chromosomal distribution. The
differences in chromosomal distribution coincided with variation in the integrase
C-terminus sequences possessing a putative targeting domain (PTD). A majority of the
group A elements possess the CR motif and are concentrated in the centromeric region,
while members of group C have the type II chromodomain and are dispersed throughout
the genome. Although representatives of the group B lack a PTD of any type, they appeared
to be localized preferentially in the centromeres of tested species. All tested elements
were found to be transcriptionally active.

Conclusions

Comprehensive analysis of the CRM clade elements showed that genuinely centromeric
retrotransposons represent only a fraction of the CRM clade (group A). These centromeric
retrotransposons represent an active component of centromeres of a wide range of angiosperm
species, implying that they play an important role in plant centromere evolution.
In addition, their transcriptional activity is consistent with the notion that the
transcription of centromeric retrotransposons has a role in normal centromere function.